Using pathogen sequence data

Los Alamos National Laboratory is
trying to increase the knowledge of
specific biological agents that terrorists
might use. Researchers are working to
develop biological and computational
tools to assist in identifying the biological "signatures" that will allow rapid identification of these agents.

The Los Alamos effort provides bioinformatics support to the
researchers of the U.S. Department of Energy's Chemical and Biological
National Security Program. Los Alamos researchers are studying
Yersinia pestis, the bacteria responsible for plague, and Bacillus
anthracis, the source of anthrax, and are beginning to study other threat
agents. In collaboration with others, this work may lead to better
methods of treatment and prevention of major illnesses. In addition, this work is likely to lead to better methods of performing forensic and
epidemiological analysis of biological incidents, determining whether
an outbreak is natural or engineered and providing a possible identity
to perpetrators.

The team also is developing various computational tools to assist in this
project. They have developed interactive visualization tools; repeat-
analysis tools; and a body of practices and procedures for data exchange
that allow researchers to perform analyses more efficiently and
exchange data more readily. The project also contributes to the
challenge of improving the integration and interoperability of large
software systems dealing with large
amounts of data.

The bioinformatics work is
distinctly a team effort. The
members work closely with the
best researchers who are investigating the organisms of particular interest to them, regardless of
affiliation. The team is working with researchers at Lawrence
Livermore National Laboratory on bacterial threat agents, with the U.S. Army Medical Research Institute of Infectious Diseases and the
University of Alabama on pox viruses. This work also is coordinated
closely with Los Alamos work on sexually transmitted diseases being
done for the National Institutes of Health. The NIH work is being done
in collaboration with world experts on herpes, papilloma and
chlamydia viruses and others.

Said team member Murray Wolinsky of the Lab 's Bioscience Division,
"Because of the large need for tools and the limited funds available, we
have to avoid 'reinventing the wheel' and use existing tools whenever
feasible. For all of these reasons, we stay abreast of the work being
done here and elsewhere and focus our efforts on unmet current and
future needs."

Such coordination helps ensure that the Lab project uses best practices
in sequence annotation and develops tools needed by the community
in general.

The Department of Energy's Office of Science is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time.